GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Maridesulfovibrio bastinii DSM 16055

Found 166 low-confidence and 57 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate kgtP: 2-oxoglutarate:H+ symporter KgtP
4-hydroxybenzoate adh: acetaldehyde dehydrogenase (not acylating) G496_RS0108130 G496_RS0115120
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase G496_RS0118200
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK
4-hydroxybenzoate pobA: 4-hydroxybenzoate 3-monooxygenase
4-hydroxybenzoate praA: protocatechuate 2,3-dioxygenase
4-hydroxybenzoate xylF: 2-hydroxymuconate semialdehyde hydrolase
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase G496_RS0113305
arabinose araE: L-arabinose:H+ symporter
arginine arcA: arginine deiminase
arginine braC: ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC G496_RS0106330 G496_RS0118025
arginine braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) G496_RS0118030 G496_RS0106325
arginine braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) G496_RS0118035 G496_RS0106320
arginine braF: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) G496_RS0118040 G496_RS0106335
asparagine aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) G496_RS0112760 G496_RS0101210
asparagine aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP G496_RS0112765 G496_RS0117885
asparagine aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) G496_RS19720 G496_RS0117895
asparagine ans: asparaginase G496_RS0108710
aspartate aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) G496_RS0112760 G496_RS0101210
aspartate aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP G496_RS0112765 G496_RS0117885
aspartate aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) G496_RS19720 G496_RS0117895
cellobiose cbp: cellobiose phosphorylase
cellobiose cdt: cellobiose transporter cdt-1/cdt-2
cellobiose glk: glucokinase G496_RS0103875
citrate citT: citrate:succinate antiporter CitT G496_RS0101965
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component G496_RS0100230 G496_RS0106055
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 G496_RS0100235 G496_RS0118315
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 G496_RS0117895 G496_RS0118315
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component G496_RS0109480 G496_RS0112080
D-alanine dadA: D-alanine dehydrogenase
D-alanine Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component G496_RS0112750
D-alanine Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component G496_RS0112765 G496_RS0117885
D-lactate D-LDH: D-lactate dehydrogenase G496_RS0115135 G496_RS0106455
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase G496_RS0108195
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) G496_RS0108130 G496_RS0115120
deoxyinosine deoB: phosphopentomutase G496_RS0104465 G496_RS0110560
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate aacS: acetoacetyl-CoA synthetase G496_RS0116710
deoxyribonate atoB: acetyl-CoA C-acetyltransferase
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate garK: glycerate 2-kinase G496_RS0105135
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose adh: acetaldehyde dehydrogenase (not acylating) G496_RS0108130 G496_RS0115120
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
ethanol adh: acetaldehyde dehydrogenase (not acylating) G496_RS0108130 G496_RS0115120
fructose 1pfk: 1-phosphofructokinase
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
fucose fucA: L-fuculose-phosphate aldolase FucA G496_RS0113305
fucose fucI: L-fucose isomerase FucI
fucose fucK: L-fuculose kinase FucK
fucose fucP: L-fucose:H+ symporter FucP
fucose fucU: L-fucose mutarotase FucU
galactose galK: galactokinase (-1-phosphate forming)
galactose galP: galactose:H+ symporter GalP
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galacturonate eda: 2-keto-3-deoxygluconate 6-phosphate aldolase
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate kdgK: 2-keto-3-deoxygluconate kinase
galacturonate uxaA: D-altronate dehydratase G496_RS0106030
galacturonate uxaB: tagaturonate reductase
galacturonate uxaC: D-galacturonate isomerase
gluconate gnd: 6-phosphogluconate dehydrogenase, decarboxylating
gluconate gntK: D-gluconate kinase
gluconate gntT: gluconate:H+ symporter GntT
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE)
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) G496_RS0110955
glucose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate garK: glycerate 2-kinase G496_RS0105135
glucuronate garR: tartronate semialdehyde reductase G496_RS0108645
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate udh: D-glucuronate dehydrogenase
glutamate aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) G496_RS0112760 G496_RS0101210
glutamate aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP G496_RS0112765 G496_RS0117885
glutamate aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) G496_RS19720 G496_RS0117895
glycerol dhaD: glycerol dehydrogenase G496_RS0111125 G496_RS0107910
glycerol dhaM: dihydroxyacetone:PEP phosphotransferase, subunit M G496_RS0112790
histidine aapM: L-histidine ABC transporter, permease component 2 (AapM) G496_RS0112760 G496_RS0101210
histidine aapP: L-histidine ABC transporter, ATPase component AapP G496_RS0112765 G496_RS0117885
histidine aapQ: L-histidine ABC transporter, permease component 1 (AapQ) G496_RS19720 G496_RS0101210
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutU: urocanase
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase
isoleucine dddA: 3-hydroxypropionate dehydrogenase G496_RS0108125
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase
isoleucine fadA: 2-methylacetoacetyl-CoA thiolase
isoleucine hpcD: 3-hydroxypropionyl-CoA dehydratase
isoleucine iolA: malonate semialdehyde dehydrogenase (CoA-acylating) G496_RS0108130 G496_RS0110290
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase G496_RS0117155
isoleucine livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) G496_RS0118030 G496_RS0106325
isoleucine livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) G496_RS0118025 G496_RS0106330
isoleucine pco: propanyl-CoA oxidase G496_RS0109315
isoleucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose glk: glucokinase G496_RS0103875
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
leucine aacS: acetoacetyl-CoA synthetase G496_RS0116710
leucine atoB: acetyl-CoA C-acetyltransferase
leucine liuA: isovaleryl-CoA dehydrogenase
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit G496_RS0107285 G496_RS0109620
leucine liuC: 3-methylglutaconyl-CoA hydratase
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine livH: L-leucine ABC transporter, permease component 1 (LivH/BraD) G496_RS0118030 G496_RS0106325
leucine livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) G496_RS0118025 G496_RS0106330
leucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
lysine amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) G496_RS0108130 G496_RS0115155
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase G496_RS0103350
lysine lysN: 2-aminoadipate transaminase G496_RS0114610 G496_RS0104745
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase G496_RS0106455
maltose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
maltose susB: alpha-glucosidase (maltase)
mannitol mtlA: mannitol phosphotransferase system, EII-CBA components
mannitol mtlD: mannitol-1-phosphate 5-dehydrogenase
mannose manA: mannose-6-phosphate isomerase G496_RS0108750
mannose manP: mannose PTS system, EII-CBA components
myoinositol iolB: 5-deoxy-D-glucuronate isomerase
myoinositol iolC: 5-dehydro-2-deoxy-D-gluconate kinase
myoinositol iolD: 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase
myoinositol iolE: scyllo-inosose 2-dehydratase
myoinositol iolG: myo-inositol 2-dehydrogenase
myoinositol iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase G496_RS0112275
myoinositol iolT: myo-inositol:H+ symporter
myoinositol mmsA: malonate-semialdehyde dehydrogenase G496_RS0108130 G496_RS0110290
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) G496_RS0110955
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components
phenylacetate paaA: phenylacetyl-CoA 1,2-epoxidase, subunit A
phenylacetate paaB: phenylacetyl-CoA 1,2-epoxidase, subunit B
phenylacetate paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C
phenylacetate paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E
phenylacetate paaF: 2,3-dehydroadipyl-CoA hydratase
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase G496_RS0117155
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aacS: acetoacetyl-CoA synthetase G496_RS0116710
phenylalanine atoB: acetyl-CoA C-acetyltransferase
phenylalanine fahA: fumarylacetoacetate hydrolase G496_RS0114085
phenylalanine hmgA: homogentisate dioxygenase
phenylalanine HPD: 4-hydroxyphenylpyruvate dioxygenase
phenylalanine livF: L-phenylalanine ABC transporter, ATPase component 1 (LivF) G496_RS0106315 G496_RS0118045
phenylalanine livG: L-phenylalanine ABC transporter, ATPase component 2 (LivG) G496_RS0106335 G496_RS0118040
phenylalanine livH: L-phenylalanine ABC transporter, permease component 1 (LivH) G496_RS0118030 G496_RS0106325
phenylalanine livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK G496_RS0118025 G496_RS0106330
phenylalanine maiA: maleylacetoacetate isomerase
phenylalanine PAH: phenylalanine 4-monooxygenase
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase
phenylalanine QDPR: 6,7-dihydropteridine reductase
proline aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) G496_RS0112760 G496_RS0101210
proline aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP G496_RS0112765 G496_RS0117885
proline aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) G496_RS19720 G496_RS0117895
proline put1: proline dehydrogenase G496_RS0110290
propionate dddA: 3-hydroxypropionate dehydrogenase G496_RS0108125
propionate hpcD: 3-hydroxypropionyl-CoA dehydratase
propionate iolA: malonate semialdehyde dehydrogenase (CoA-acylating) G496_RS0108130 G496_RS0110290
propionate pco: propanyl-CoA oxidase G496_RS0109315
putrescine gabT: gamma-aminobutyrate transaminase G496_RS0103350 G496_RS0100990
putrescine patA: putrescine aminotransferase (PatA/SpuC) G496_RS0109520 G496_RS0112560
putrescine patD: gamma-aminobutyraldehyde dehydrogenase G496_RS0108130 G496_RS0114360
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose rhaA: L-rhamnose isomerase
rhamnose rhaB: L-rhamnulokinase
rhamnose rhaD: rhamnulose 1-phosphate aldolase
rhamnose rhaM: L-rhamnose mutarotase
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsK: ribokinase
ribose rbsU: probable D-ribose transporter RbsU
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase G496_RS0117155
sucrose scrK: fructokinase
sucrose SUS: sucrose synthase
sucrose sut: sucrose:proton symporter SUT/SUC
threonine adh: acetaldehyde dehydrogenase (not acylating) G496_RS0108130 G496_RS0115120
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) G496_RS0100925 G496_RS0100920
threonine lpd: dihydrolipoyl dehydrogenase G496_RS0100915 G496_RS0103870
thymidine adh: acetaldehyde dehydrogenase (not acylating) G496_RS0108130 G496_RS0115120
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase G496_RS0104465 G496_RS0110560
thymidine nupG: thymidine permease NupG/XapB
trehalose glk: glucokinase G496_RS0103875
trehalose PsTP: trehalose phosphorylase
trehalose TRET1: facilitated trehalose transporter Tret1
tryptophan tnaA: tryptophanase
tyrosine aacS: acetoacetyl-CoA synthetase G496_RS0116710
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine atoB: acetyl-CoA C-acetyltransferase
tyrosine fahA: fumarylacetoacetate hydrolase G496_RS0114085
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase
valine bch: 3-hydroxyisobutyryl-CoA hydrolase
valine dddA: 3-hydroxypropionate dehydrogenase G496_RS0108125
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase
valine hpcD: 3-hydroxypropionyl-CoA dehydratase
valine iolA: malonate semialdehyde dehydrogenase (CoA-acylating) G496_RS0108130 G496_RS0110290
valine livH: L-valine ABC transporter, permease component 1 (LivH/BraD) G496_RS0118030 G496_RS0106325
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) G496_RS0118025 G496_RS0106330
valine mmsA: methylmalonate-semialdehyde dehydrogenase G496_RS0114360 G496_RS0110290
valine mmsB: 3-hydroxyisobutyrate dehydrogenase G496_RS0108645
valine pco: propanyl-CoA oxidase G496_RS0109315
valine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase G496_RS0111045 G496_RS0102495
xylose xylA: xylose isomerase
xylose xylB: xylulokinase
xylose xylT: D-xylose transporter

Confidence: high confidence medium confidence low confidence

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory